DOCSLIB.ORG

Reconstructing Unrooted Phylogenetic Trees from Symbolic Ternary Metrics

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Reconstructing Unrooted Phylogenetic Trees from Symbolic Ternary Metrics Reconstructing unrooted phylogenetic trees from symbolic ternary metrics Stefan Gr¨unewald CAS-MPG Partner Institute for Computational Biology Chinese Academy of Sciences Key Laboratory of Computational Biology 320 Yue Yang Road, Shanghai 200032, China Email: [email protected] Yangjing Long School of Mathematics and Statistics Central China Normal University, Luoyu Road 152, Wuhan, Hubei 430079, China Email: [email protected] Yaokun Wu Department of Mathematics and MOE-LSC Shanghai Jiao Tong University Dongchuan Road 800, Shanghai 200240, China Email: [email protected] Abstract In 1998, B¨ocker and Dress presented a 1-to-1 correspondence between symbolically dated rooted trees and symbolic ultrametrics. We consider the corresponding problem for unrooted trees. More precisely, given a tree T with leaf set X and a proper vertex coloring of its interior vertices, we can map every triple of three different leaves to the color of its median vertex. We characterize all ternary maps that can be obtained in this way in terms of 4- and 5-point conditions, and we show that the corresponding tree and its coloring can be reconstructed from a ternary map that satisfies those conditions. Further, we give an additional condition that characterizes whether the tree is binary, and we describe an algorithm that reconstructs general trees in a bottom-up fashion. Keywords: symbolic ternary metric ; median vertex ; unrooted phylogenetic tree 1 Introduction A phylogenetic tree is a rooted or unrooted tree where the leaves are labeled by some objects of interest, usually taxonomic units (taxa) like species. The edges have a positive edge length, thus the tree defines a metric on the taxa set. It is a classical result in phylogenetics that the tree can be reconstructed from this metric, if it is unrooted or ultrametric. The latter means that the tree is rooted and all taxa are equally far away from the root. An ultrametric tree is realistic whenever the edge lengths are proportional to time and the taxa are species that can be observed in the present. In an ultrametric tree, the distance between arXiv:1702.00190v3 [math.CO] 17 Jan 2018 two taxa is twice of the distance between each of the taxa and their last common ancestor (lca), hence pairs of taxa with the same lca must have the same distance. For three taxa x; y; z, it follows that there is no unique maximum within their three pairwise distances, thus we have d(x; y) ≤ maxfd(x; z); d(y; z)g. This 3-point condition turns out to be sufficient for a metric to be ultrametric, too, and it is the key for reconstructing ultrametric trees from their distances. In 1995, Bandelt and Steel [1] observed that the complete ordering of the real numbers is not necessary to reconstruct trees, and they showed that the real-valued distances can be replaced by maps from the pairs of taxa into a cancellative abelian monoid. Later, B¨ocker and Dress [2] pushed this idea to the limit by proving that the image set of the symmetric map does not need any structure at all (see Section 2 for details). While this result is useful for understanding how little information it takes to reconstruct an ultrametric phylogenetic tree, it was not until recently that it turned out to have some practical applications. In 2013, Hellmuth et al. [8] found an alternative characterization of symbolic ultrametrics in terms of cographs and showed that, for perfect data, phylogenetic trees can be reconstructed from orthology information. By adding some optimization tools, this concept was then applied to analyze real data [9]. Motivated by the practical applicability of symbolic ultrametrics, we are considering their unrooted version. However, in an unrooted tree there is in general no interior vertex associated to a pair of taxa that would correspond to the last common ancestor in a rooted tree. Instead, there is a median associated 1 to every set of three taxa that represents, for every possible rooting of the tree, a last common ancestor of at least two of the three taxa. Therefore, we consider ternary maps from the triples of taxa into an image set without any structure. We will show that an unrooted phylogenetic tree with a proper vertex coloring can be reconstructed from the function that maps every triple of taxa to the color of its median. In order to apply our results to real data, we need some way to assign a state to every set of three taxa, with the property that 3-sets with the same median will usually have the same state. For symbolic ultrametrics, the first real application was found 15 years after the development of the theory. In addition to the hope that something similar happens with symbolic ternary metrics, we have some indication that they can be useful to construct unrooted trees from orthology relations (see Section 6. Consider an unrooted tree T with vertex set V , edge set E, and leaf set X, and a dating map t : V ! M , where M = M [ { } such that t(x) = for all x 2 X, and t(v1) 6= t(v2) if v1v2 2 E. V For any S = fx; yg 2 2 there is a unique path [x; y] with end points x and y, and for any 3-set V S = fx; y; zg 2 3 there is a unique triple point or median med(x; y; z) such that [x; y] \ [y; z] \ [x; z] = fmed(x; y; z)g. Putting [x; x] = fxg, the definition also works, if some or all of x; y and z equal. Given a phylogenetic tree T on X and a dating map t : V ! M , we can define the symmetric symbolic ternary map d(T ;t) : X × X × X ! M by d(T ;t)(x; y; z) = t(med(x; y; z)). In this set-up, our question can be phrased as follows: Suppose we are given an arbitrary symbolic ternary map δ : X × X × X ! M , can we determine if there is a pair (T ; t) for which d(T :t)(x; y; z) = δ(x; y; z) holds for all x; y; z 2 X? The rest of this paper is organized as follows. In Section 1.1, we present the basic and relevant concepts used in this paper. In Section 2 we recall the one-to-one correspondence between symbolic ultrametrics and symbolically dated trees, and introduce our main results Theorem 4 and Theorem 5. In Section 3 we give the proof of Theorem 4. In order to prove our main result, we first introduce the connection between phylogenetic trees and quartet systems on X in Subsection 3.1. Then we use a graph representation to analyze all cases of the map δ for 5-taxa subsets of X in Subsection 3.2. In Section 4 we use a similar method to prove Theorem 5, which gives a sufficient and necessary condition to reconstruct a binary phylogenetic tree on X. In Section 5, we give a criterion to identify all pseudo-cherries of the underlying tree from a symbolic ternary metric. This result makes it possible to reconstruct the tree in a bottom-up fashion. In the last section we discuss some open questions and future work. 1.1 Preliminaries We introduce the relevant basic concepts and notation. Unless stated otherwise, we will follow the monographs [11] and [4]. In the remainder of this paper, X denotes a finite set of size at least three. An (unrooted) tree T = (V; E) is an undirected connected acyclic graph with vertex set V and edge set E. A vertex of T is a leaf if it is of degree 1, and all vertices with degree at least two are interior vertices. A rooted tree T = (V; E) is a tree that contains a distinguished vertex ρT 2 V called the root. We define a partial order T on V by setting v T w for any two vertices v; w 2 V for which v is a vertex on the path from ρT to w. In particular, if v T w and v 6= w we call v an ancestor of w. An unrooted phylogenetic tree T on X is an unrooted tree with leaf set X that does not contain any vertex of degree 2. It is binary, if every interior vertex has degree 3. A rooted phylogenetic tree T on X is a rooted tree with leaf set X that does not contain any vertices with in- and out-degree one, and whose root ρT has in-degree zero. For a set A ⊆ X with cardinality at least 2, we define the last common ancestor of A, denoted by lcaT (A), to be the unique vertex in T that is the greatest lower bound of A under the partial order T . In case A = fx; yg we put lcaT (x; y) = lcaT (fx; yg). Given a set Q of four taxa fa; b; c; dg, there exist always exactly three partitions into two pairs: ffa; bg; fc; dgg,ffa; cg; fb; dgg and ffa; dg; fb; cgg. These partitions are called quartets, and they represent the three non-isomorphic unrooted binary trees with leaf set Q. These trees are usually called quartet trees, and they { as well as the corresponding quartets {are symbolized by abjcd; acjbd; adjbc respectively. We use Q(X) to denote the set of all quartets with four taxa in X. A phylogenetic tree T on X displays a quartet abjcd 2 Q(X), if the path from a to b in T is vertex-disjoint with the path from c to d.
Load more

Recommended publications
  • Helly Property and Satisfiability of Boolean Formulas Defined on Set
    Helly Property and Satisfiability of Boolean Formulas Defined on Set Systems Victor Chepoi Nadia Creignou LIF (CNRS, UMR 6166) LIF (CNRS, UMR 6166) Universit´ede la M´editerran´ee Universit´ede la M´editerran´ee 13288 Marseille cedex 9, France 13288 Marseille cedex 9, France Miki Hermann Gernot Salzer LIX (CNRS, UMR 7161) Technische Universit¨atWien Ecole´ Polytechnique Favoritenstraße 9-11 91128 Palaiseau, France 1040 Wien, Austria March 7, 2008 Abstract We study the problem of satisfiability of Boolean formulas ' in conjunctive normal form whose literals have the form v 2 S and express the membership of values to sets S of a given set system S. We establish the following dichotomy result. We show that checking the satisfiability of such formulas (called S-formulas) with three or more literals per clause is NP-complete except the trivial case when the intersection of all sets in S is nonempty. On the other hand, the satisfiability of S-formulas ' containing at most two literals per clause is decidable in polynomial time if S satisfies the Helly property, and is NP-complete otherwise (in the first case, we present an O(j'j · jSj · jDj)-time algorithm for deciding if ' is satisfiable). Deciding whether a given set family S satisfies the Helly property can be done in polynomial time. We also overview several well-known examples of Helly families and discuss the consequences of our result to such set systems and its relationship with the previous work on the satisfiability of signed formulas in multiple-valued logic. 1 Introduction The satisfiability of Boolean formulas in conjunctive normal form (SAT problem) is a fundamental problem in theoretical computer science and discrete mathematics.
    [Show full text]
  • Solution-Graphs of Boolean Formulas and Isomorphism∗
    Journal on Satisfiability, Boolean Modeling, and Computation 10 (2019) 37-58 Solution-Graphs of Boolean Formulas and Isomorphism∗ Patrick Scharpfeneckery [email protected] Jacobo Tor´an [email protected] University of Ulm Institute of Theoretical Computer Science Ulm, Germany Abstract The solution-graph of a Boolean formula on n variables is the subgraph of the hypercube Hn induced by the satisfying assignments of the formula. The structure of solution-graphs has been the object of much research in recent years since it is important for the performance of SAT-solving procedures based on local search. Several authors have studied connectivity problems in such graphs focusing on how the structure of the original formula might affect the complexity of the connectivity problems in the solution-graph. In this paper we study the complexity of the isomorphism problem of solution-graphs of Boolean formulas. We consider the classes of formulas that arise in the CSP-setting and investigate how the complexity of the isomorphism problem depends on the formula type. We observe that for general formulas the solution-graph isomorphism problem can be solved in exponential time while in the cases of 2CNF formulas, as well as for CPSS formulas, the problem is in the counting complexity class C=P, a subclass of PSPACE. We also prove a strong property on the structure of solution-graphs of Horn formulas showing that they are just unions of partial cubes. In addition, we give a PSPACE lower bound for the problem on general Boolean functions. We prove that for 2CNF, as well as for CPSS formulas the solution-graph isomorphism problem is hard for C=P under polynomial time many-one reductions, thus matching the given upper bound.
    [Show full text]
  • A Convexity Lemma and Expansion Procedures for Bipartite Graphs
    Europ. J. Combinatorics (1998) 19, 677±685 Article No. ej980229 A Convexity Lemma and Expansion Procedures for Bipartite Graphs WILFRIED IMRICH AND SANDI KLAVZARÏ ² A hierarchy of classes of graphs is proposed which includes hypercubes, acyclic cubical com- plexes, median graphs, almost-median graphs, semi-median graphs and partial cubes. Structural properties of these classes are derived and used for the characterization of these classes by expan- sion procedures, for a characterization of semi-median graphs by metrically de®ned relations on the edge set of a graph and for a characterization of median graphs by forbidden subgraphs. Moreover, a convexity lemma is proved and used to derive a simple algorithm of complexity O(mn) for recognizing median graphs. c 1998 Academic Press 1. INTRODUCTION Hamming graphs and related classes of graphs have been of continued interest for many years as can be seen from the list of references. As the subject unfolded, many interesting problems arose which have not been solved yet. In particular, it is still open whether the known algorithms for recognizing partial cubes or median graphs, which comprise an important subclass of partial cubes, are optimal. The best known algorithms for recognizing whether a graph G is a member of the class of partial cubes have complexity O(mn), where m and n denote, respectively, the numbersPC of edges and vertices of G, see [1, 13]. As the recognition process involves a coloring of the edges of G, which is a special case of sorting, one might be tempted to look for an algorithm of complexity O(m log n).
    [Show full text]
  • Steps in the Representation of Concept Lattices and Median Graphs Alain Gély, Miguel Couceiro, Laurent Miclet, Amedeo Napoli
    Steps in the Representation of Concept Lattices and Median Graphs Alain Gély, Miguel Couceiro, Laurent Miclet, Amedeo Napoli To cite this version: Alain Gély, Miguel Couceiro, Laurent Miclet, Amedeo Napoli. Steps in the Representation of Concept Lattices and Median Graphs. CLA 2020 - 15th International Conference on Concept Lattices and Their Applications, Sadok Ben Yahia; Francisco José Valverde Albacete; Martin Trnecka, Jun 2020, Tallinn, Estonia. pp.1-11. hal-02912312 HAL Id: hal-02912312 https://hal.inria.fr/hal-02912312 Submitted on 5 Aug 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Steps in the Representation of Concept Lattices and Median Graphs Alain Gély1, Miguel Couceiro2, Laurent Miclet3, and Amedeo Napoli2 1 Université de Lorraine, CNRS, LORIA, F-57000 Metz, France 2 Université de Lorraine, CNRS, Inria, LORIA, F-54000 Nancy, France 3 Univ Rennes, CNRS, IRISA, Rue de Kérampont, 22300 Lannion, France {alain.gely,miguel.couceiro,amedeo.napoli}@loria.fr Abstract. Median semilattices have been shown to be useful for deal- ing with phylogenetic classication problems since they subsume me- dian graphs, distributive lattices as well as other tree based classica- tion structures. Median semilattices can be thought of as distributive _-semilattices that satisfy the following property (TRI): for every triple x; y; z, if x ^ y, y ^ z and x ^ z exist, then x ^ y ^ z also exists.
    [Show full text]
  • Graphs of Acyclic Cubical Complexes
    Europ . J . Combinatorics (1996) 17 , 113 – 120 Graphs of Acyclic Cubical Complexes H A N S -J U ¨ R G E N B A N D E L T A N D V I C T O R C H E P O I It is well known that chordal graphs are exactly the graphs of acyclic simplicial complexes . In this note we consider the analogous class of graphs associated with acyclic cubical complexes . These graphs can be characterized among median graphs by forbidden convex subgraphs . They possess a number of properties (in analogy to chordal graphs) not shared by all median graphs . In particular , we disprove a conjecture of Mulder on star contraction of median graphs . A restricted class of cubical complexes for which this conjecture would hold true is related to perfect graphs . ÷ 1996 Academic Press Limited 1 . C U B I C A L C O M P L E X E S A cubical complex is a finite set _ of (graphic) cubes of any dimensions which is closed under taking subcubes and non-empty intersections . If we replace each cube of _ by a solid cube , then we obtain the geometric realization of _ , called a cubical polyhedron ; for further information consult van de Vel’s book [18] . Vertices of a cubical complex _ are 0-dimensional cubes of _ . In the ( underlying ) graph G of the complex two vertices of _ are adjacent if they constitute a 1-dimensional cube . Particular cubical complexes arise from median graphs . In what follows we consider only finite graphs .
    [Show full text]
  • Discrete Mathematics Cube Intersection Concepts in Median
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Discrete Mathematics 309 (2009) 2990–2997 Contents lists available at ScienceDirect Discrete Mathematics journal homepage: www.elsevier.com/locate/disc Cube intersection concepts in median graphsI Bo²tjan Bre²ar a,∗, Tadeja Kraner Šumenjak b a FEECS, University of Maribor, Smetanova 17, 2000 Maribor, Slovenia b FA, University of Maribor, Vrbanska 30, 2000 Maribor, Slovenia article info a b s t r a c t Article history: In this paper, we study different classes of intersection graphs of maximal hypercubes Received 24 September 2007 of median graphs. For a median graph G and k ≥ 0, the intersection graph Qk.G/ Received in revised form 27 July 2008 is defined as the graph whose vertices are maximal hypercubes (by inclusion) in G, Accepted 29 July 2008 and two vertices H and H in Q .G/ are adjacent whenever the intersection H \ H Available online 30 August 2008 x y k x y contains a subgraph isomorphic to Qk. Characterizations of clique-graphs in terms of these Keywords: intersection concepts when k > 0, are presented. Furthermore, we introduce the so- Cartesian product called maximal 2-intersection graph of maximal hypercubes of a median graph G, denoted Median graph Qm2.G/, whose vertices are maximal hypercubes of G, and two vertices are adjacent if the Cube graph intersection of the corresponding hypercubes is not a proper subcube of some intersection Intersection graph of two maximal hypercubes. We show that a graph H is diamond-free if and only if there Convexity exists a median graph G such that H is isomorphic to Qm2.G/.
    [Show full text]
  • A Self-Stabilizing Algorithm for the Median Problem in Partial Rectangular Grids and Their Relatives1
    A self-stabilizing algorithm for the median problem in partial rectangular grids and their relatives1 Victor Chepoi, Tristan Fevat, Emmanuel Godard and Yann Vaxes` LIF-Laboratoire d’Informatique Fondamentale de Marseille, CNRS (UMR 6166), Universit´ed’Aix-Marseille, Marseille, France {chepoi,fevat,godard,vaxes}@lif.univ-mrs.fr Abstract. Given a graph G = (V, E), a vertex v of G is a median vertex if it minimizes the sum of the distances to all other vertices of G. The median problem consists of finding the set of all median vertices of G. In this note, we present self-stabilizing algorithms for the median problem in partial rectangular grids and relatives. Our algorithms are based on the fact that partial rectangular grids can be isometrically embedded into the Cartesian product of two trees, to which we apply the algorithm proposed by Antonoiu, Srimani (1999) and Bruell, Ghosh, Karaata, Pemmaraju (1999) for computing the medians in trees. Then we extend our approach from partial rectangular grids to a more general class of plane quadrangulations. We also show that the characterization of medians of trees given by Gerstel and Zaks (1994) extends to cube-free median graphs, a class of graphs which includes these quadrangulations. 1 Introduction Given a connected graph G one is sometimes interested in finding the vertices minimizing the total distance Pu d(u, x) to the vertices u of G, where d(u, x) is the distance between u and x. A vertex x minimizing this expression is called a median (vertex) of G. The median problem consists of finding the set of all median vertices.
    [Show full text]
  • Lecture 6 1 Nonexpansive Maps
    Hypercube problems Lecture 6 November 14, 2012 Lecturer: Petr Gregor Scribe by: V´aclav Vlˇcek Updated: January 22, 2013 1 Nonexpansive maps Definition 1 (nonexpansive map) Let G and H be graphs. A mapping f : V (G) ! V (H) is called nonexpansive if dH (f(u); f(v)) dG(u; v) for every x; y V (G) (i.e. it does not increase distances). ≤ 2 Nonexpansive maps are also known as weak homomorphisms, mappings satisfying the property that for every xy E(G): f(x)f(y) E(H) or f(x) = f(y). Equivalence of these 2 2 two notions is easy to see, as weak homomorphism can not prolong any path and vice-versa, nonexpansive maps do not increase distance of adjacent vertices. A nonexpansive map of G to G is called simply a nonexpansive map on G. It is easy to see that composition of two nonexpansive mappings is also nonexpansive and that image f(G) of a connected graph G under a nonexpansive map f is also connected. Definition 2 (fixed point, periodic point) Let f be a (nonexpansive) map on G. We say that x is a fixed point of f if f(x) = x. We denote the set of all fixed points of f by fix(f). We say that x is a periodic point of f if f (p)(x) = x for some p 1. The smallest ≥ such p is the period of x. We denote the set of all periodic points by per(f). Definition 3 (retraction, weak retraction) A retraction (weak retraction) on G is an endomorphism (nonexpansive map, respectively) f : V (G) V (G) such that f (2)(x) = f(x) ! for every x (this property is called idempotence).
    [Show full text]
  • Metric Graph Theory and Geometry: a Survey
    Contemporary Mathematics Metric graph theory and geometry: a survey Hans-JÄurgenBandelt and Victor Chepoi Abstract. The article surveys structural characterizations of several graph classes de¯ned by distance properties, which have in part a general algebraic flavor and can be interpreted as subdirect decomposition. The graphs we feature in the ¯rst place are the median graphs and their various kinds of generalizations, e.g., weakly modular graphs, or ¯ber-complemented graphs, or l1-graphs. Several kinds of l1-graphs admit natural geometric realizations as polyhedral complexes. Particular instances of these graphs also occur in other geometric contexts, for example, as dual polar graphs, basis graphs of (even ¢-)matroids, tope graphs, lopsided sets, or plane graphs with vertex degrees and face sizes bounded from below. Several other classes of graphs, e.g., Helly graphs (as injective objects), or bridged graphs (generalizing chordal graphs), or tree-like graphs such as distance-hereditary graphs occur in the investigation of graphs satisfying some basic properties of the distance function, such as the Helly property for balls, or the convexity of balls or of the neighborhoods of convex sets, etc. Operators between graphs or complexes relate some of the graph classes reported in this survey. 0. Introduction Discrete geometry involves ¯nite con¯gurations of points, lines, planes or other geometric objects, with the emphasis on combinatorial properties (Matou·sek[139]). This leads to a number of intriguing problems - indeed, \the subject of combina- torics is devoted to the study of structures on a ¯nite set; many of the most interest- ing of these structures arise from elimination of continuous parameters in problems from other mathematical disciplines" (Borovik et al.
    [Show full text]
  • Raticky' in a Distributive Lattice L One Can Define a Ternary Operation Wt
    Discrete Mathematics45 (1983) l-30 North-Holland Publishing Company Hans-J. BANDELT Fachbereich6 der Uniuersitiit Oldenburg, D-Z!XM OZd&urg, BRD Jarmila HEDLkOVA Mrat~~raticky’tistav SAV, Obrancou mieru 49, 886 25 Bratislavn, &$I? Received 30 August 1980 A median algebra is a ternary algebra which satisfies all the identities true for the median operation in d%tribuGve lattices. The relationship of median algebras to (abstract) geometries, graphs, and semilattices is discussed in detail. In particular, all intrinsic semilattice orders on a median algebra are exhibited and characterized in several ways. In a distributive lattice L one can define a ternary operation wt : L3 * L by m(e, b,c)=(ah)v(a~c)v(b/w)=(avb)~(avc)A(bvc), ~7~Gch is usually referred to as the median operation in L. Several prcperties of a distributive lattice are reflected by its median m. For instance, if two distributive lattices defined on a set L have the same convex sublattices or the same congruences, then their median operations coincide. In other words, convex sublattices and congruences are median invariants. Moreover, the Hasse diagram (regarded as an undirected graph) of a distributive lattice with finite intervals depends only on the median. All this suggests an ‘abstract’ study of the median operation: a median algebra is an algebra with a single ternary operation m which satisfies all the identities true for the median operation in distributive lattices. As trees show median algebras are in general not induced by distributive lattices; nevertheless, they can be embedded into distributive lattices. Every median algebra M is endowed with several ‘compatible’ szmilattice orders, e.g.
    [Show full text]
  • On the Complexity of Recognizing Hamming Graphs and Related Classes of Graphs
    Europ . J . Combinatorics (1996) 17 , 209 – 221 On the Complexity of Recognizing Hamming Graphs and Related Classes of Graphs W ILFRIED I MRICH AND S ANDI K LAVZ ä AR This paper contains a new algorithm that recognizes whether a given graph G is a Hamming graph , i . e . a Cartesian product of complete graphs , in O ( m ) time and O ( n 2 ) space . Here m and n denote the numbers of edges and vertices of G , respectively . Previously this was only possible in O ( m log n ) time . Moreover , we present a survey of other recognition algorithms for Hamming graphs , retracts of Hamming graphs and isometric subgraphs of Hamming graphs . Special emphasis is also given to the bipartite case in which these classes are reduced to binary Hamming graphs , median graphs and partial binary Hamming graphs . ÷ 1996 Academic Press Limited 1 . I NTRODUCTION This paper is a contribution to the recognition of classes of graphs defined by metric properties . These classes include Hamming graphs , quasi-median graphs , partial Hamming graphs , binary Hamming graphs , median graphs and partial binary Hamming graphs . We shall define the above-mentioned classes of graphs , list some of their structural properties , in particular those which are exploited from the algorithmic point of view , and then shortly describe the ideas behind several recognition algorithms . Moreover , we also present a new recognition algorithm which is optimal in its time complexity for the recognition of Hamming graphs . All graphs considered in this paper are finite undirected graphs without loops or multiple edges . Throughout the paper , for a given graph G , let n and m denote the number of its vertices and edges , respectively .
    [Show full text]
  • Diameter in Linear Time for Constant-Dimension Median Graphs
    Diameter in linear time for constant-dimension median graphs Pierre Bergé1, Michel Habib1 IRIF, CNRS, Université de Paris [email protected], [email protected] Mots-clés : Diameter, Median graphs, Hypercubes. 1 Contribution We study here one of the most fundamental problems in algorithmic graph theory related to distances : the diameter. Given an n-vertex undirected graph G = (V, E), the diameter is the maximum distance d(u, v), u, v ∈ V , where d(u, v) is the length of shortest (u, v)-paths. It is a basic parameter used to apprehend the structure of a graph. In this paper, we propose a linear-time algorithm computing the diameter of constant- dimension median graphs. Median graphs form the class of graphs which is certainly the most studied in metric graph theory. They are the graphs such that any triplet of vertices has a unique median. Put formally, given x, y, z ∈ V , there is a unique vertex m(x, y, z) lying at the same time on some shortest (x, y), (y, z), and (z, x)-paths. Said differently, m(x, y, z) is the unique vertex being metrically between x and y, y and z, z and x. Median graphs are partial cubes, i.e. isometric subgraphs of hypercubes. However, partial cubes are not necessarily me- dian. Furthermore, median graphs are triangle-free, bipartite and do not contain induced K2,3. The dimension d of a median graph is the dimension of its largest induced hypercube. This parameter is upper-bounded by blog nc. To the best of our knowledge, there is no subquadratic algorithm for the diameter on median graphs.
    [Show full text]